# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 08:21:40 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 4-(1,3-benzodioxol-5-yloxy)-2-[4-(1H-imidazol-1-yl)phenoxy]-6-methylpyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Oc2ccc3OCOc3c2)nc(Oc4ccc(cc4)n5ccnc5)n1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 391  391  4-(1,3-benzodioxol-5-yloxy)-2-[4-(1H-imidazol-1-yl)phenoxy]-6-methylpyrimidine  ligand  45  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_391
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 391  C36   C  CR16  0  -0.361  -1.3447  -1.9778  -1.0872
 391  C35   C  CR56  0   0.313  -2.2411  -2.9653  -0.7738
 391  O39   O  O     0  -0.486  -2.8402  -3.8506  -1.6042
 391  C38   C  CH2   0   0.060  -3.8234  -4.5171  -0.8228
 391  O37   O  O     0  -0.486  -3.5200  -4.2489   0.5381
 391  C34   C  CR56  0   0.305  -2.6518  -3.2074   0.5292
 391  C33   C  CR16  0  -0.347  -2.1838  -2.4657   1.5829
 391  C32   C  CR16  0  -0.326  -1.2551  -1.4576   1.2906
 391  C31   C  CR6   0   0.336  -0.8563  -1.2319  -0.0100
 391  O28   O  O2    0  -0.507   0.0395  -0.2000  -0.2478
 391  C23   C  CR6   0   0.564   1.2913  -0.5233  -0.5873
 391  N22   N  N     0  -0.471   1.6055  -1.7931  -0.6792
 391  C24   C  CR16  0  -0.443   2.2126   0.4926  -0.8274
 391  C25   C  CR6   0   0.287   3.4888   0.0809  -1.1726
 391  C27   C  CH3   0  -0.719   4.5811   1.0650  -1.4298
 391  N26   N  N     0  -0.467   3.8081  -1.2159  -1.2924
 391  C21   C  CR6   0   0.569   2.8393  -2.0655  -1.0464
 391  O17   O  O2    0  -0.499   3.1631  -3.3622  -1.1913
 391  C14   C  CR6   0   0.344   2.1284  -4.2719  -1.0914
 391  C15   C  CR16  0  -0.297   2.0036  -5.0278   0.0586
 391  C16   C  CR16  0  -0.299   0.9572  -5.9309   0.1709
 391  C13   C  CR16  0  -0.276   1.2308  -4.4118  -2.1368
 391  C12   C  CR16  0  -0.287   0.1704  -5.2903  -2.0125
 391  C11   C  CR6   0   0.361   0.0294  -6.0459  -0.8547
 391  N3    N  NR5   0  -0.525  -1.0650  -6.9251  -0.7203
 391  C4    C  CR15  0  -0.111  -1.7821  -7.1711   0.4233
 391  C5    C  CR15  0  -0.216  -2.7382  -8.0741   0.0665
 391  NFE   N  N     0  -0.446  -2.6235  -8.3888  -1.2601
 391  C2    C  CR15  0   0.082  -1.6165  -7.6861  -1.7008
 391  H36   H  HCR6  0   0.283  -1.0221  -1.7948  -2.1028
 391  H381  H  HCH2  0   0.243  -3.7793  -5.5905  -1.0063
 391  H382  H  HCH2  0   0.240  -4.8175  -4.1260  -1.0667
 391  H33   H  HCR6  0   0.277  -2.5030  -2.6496   2.5994
 391  H32   H  HCR6  0   0.271  -0.8512  -0.8515   2.0905
 391  H24   H  HCR6  0   0.284   1.9505   1.5372  -0.7443
 391  H271  H  HCH3  0   0.264   5.3646   0.9573  -0.6785
 391  H272  H  HCH3  0   0.262   5.0386   0.8818  -2.4021
 391  H273  H  HCH3  0   0.252   4.2167   2.0893  -1.4017
 391  H15   H  HCR6  0   0.278   2.7142  -4.9163   0.8668
 391  H16   H  HCR6  0   0.283   0.8702  -6.5369   1.0631
 391  H13   H  HCR6  0   0.280   1.3323  -3.8133  -3.0329
 391  H12   H  HCR6  0   0.281  -0.5611  -5.3576  -2.8061
 391  H4    H  HCR5  0   0.297  -1.5705  -6.6756   1.3552
 391  H5    H  HCR5  0   0.258  -3.5025  -8.5072   0.6927
 391  H2    H  HCR5  0   0.292  -1.2249  -7.6998  -2.7067

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 391  C36  C31   aromatic  1.398  0.020  1.398
 391  C36  C35   aromatic  1.370  0.020  1.370
 391  C36  H36   single    0.930  0.020  1.080
 391  C35  O39   single    1.354  0.020  1.354
 391  C35  C34   aromatic  1.387  0.020  1.387
 391  O39  C38   single    1.422  0.020  1.422
 391  C38  O37   single    1.420  0.020  1.420
 391  C38  H381  single    0.970  0.020  1.090
 391  C38  H382  single    0.970  0.020  1.090
 391  O37  C34   single    1.356  0.020  1.356
 391  C34  C33   aromatic  1.371  0.020  1.371
 391  C33  C32   aromatic  1.401  0.020  1.401
 391  C33  H33   single    0.930  0.020  1.080
 391  C32  C31   aromatic  1.379  0.020  1.379
 391  C32  H32   single    0.930  0.020  1.080
 391  C31  O28   single    1.387  0.020  1.387
 391  O28  C23   single    1.337  0.020  1.337
 391  C23  C24   aromatic  1.392  0.020  1.392
 391  C23  N22   aromatic  1.311  0.020  1.311
 391  N22  C21   aromatic  1.316  0.020  1.316
 391  C24  C25   aromatic  1.385  0.020  1.385
 391  C24  H24   single    0.930  0.020  1.080
 391  C25  C27   single    1.493  0.020  1.493
 391  C25  N26   aromatic  1.341  0.020  1.341
 391  C27  H271  single    0.970  0.020  1.090
 391  C27  H272  single    0.970  0.020  1.090
 391  C27  H273  single    0.970  0.020  1.090
 391  N26  C21   aromatic  1.312  0.020  1.312
 391  C21  O17   single    1.344  0.020  1.344
 391  O17  C14   single    1.381  0.020  1.381
 391  C14  C15   aromatic  1.382  0.020  1.382
 391  C14  C13   aromatic  1.385  0.020  1.385
 391  C15  C16   aromatic  1.387  0.020  1.387
 391  C15  H15   single    0.930  0.020  1.080
 391  C16  C11   aromatic  1.388  0.020  1.388
 391  C16  H16   single    0.930  0.020  1.080
 391  C13  C12   aromatic  1.383  0.020  1.383
 391  C13  H13   single    0.930  0.020  1.080
 391  C12  C11   aromatic  1.390  0.020  1.390
 391  C12  H12   single    0.930  0.020  1.080
 391  C11  N3    single    1.410  0.020  1.410
 391  N3   C4    aromatic  1.372  0.020  1.372
 391  N3   C2    aromatic  1.358  0.020  1.358
 391  C4   C5    aromatic  1.363  0.020  1.363
 391  C4   H4    single    0.930  0.020  1.080
 391  C5   NFE   aromatic  1.368  0.020  1.368
 391  C5   H5    single    0.930  0.020  1.080
 391  NFE  C2    aromatic  1.305  0.020  1.305
 391  C2   H2    single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 391  H36   C36  C31   121.95  3.000
 391  H36   C36  C35   122.15  3.000
 391  C31   C36  C35   115.90  3.000
 391  C34   C35  O39   109.33  3.000
 391  C34   C35  C36   122.30  3.000
 391  O39   C35  C36   128.36  3.000
 391  C38   O39  C35   105.99  3.000
 391  H382  C38  H381  110.53  3.000
 391  H382  C38  O37   109.86  3.000
 391  H381  C38  O37   109.80  3.000
 391  H382  C38  O39   109.74  3.000
 391  H381  C38  O39   109.95  3.000
 391  O37   C38  O39   106.89  3.000
 391  C34   O37  C38   106.00  3.000
 391  C33   C34  O37   128.99  3.000
 391  C33   C34  C35   121.76  3.000
 391  O37   C34  C35   109.25  3.000
 391  H33   C33  C32   120.94  3.000
 391  H33   C33  C34   121.99  3.000
 391  C32   C33  C34   117.07  3.000
 391  H32   C32  C31   119.85  3.000
 391  H32   C32  C33   119.75  3.000
 391  C31   C32  C33   120.41  3.000
 391  O28   C31  C32   118.05  3.000
 391  O28   C31  C36   119.37  3.000
 391  C32   C31  C36   122.56  3.000
 391  C23   O28  C31   117.94  3.000
 391  C24   C23  N22   122.40  3.000
 391  N22   C23  O28   118.45  3.000
 391  C24   C23  O28   119.15  3.000
 391  C21   N22  C23   116.41  3.000
 391  H24   C24  C25   122.03  3.000
 391  H24   C24  C23   122.12  3.000
 391  C25   C24  C23   115.85  3.000
 391  N26   C25  C27   116.62  3.000
 391  N26   C25  C24   121.96  3.000
 391  C27   C25  C24   121.43  3.000
 391  H273  C27  H272  108.79  3.000
 391  H273  C27  H271  108.41  3.000
 391  H272  C27  H271  107.23  3.000
 391  H273  C27  C25   111.80  3.000
 391  H272  C27  C25   110.49  3.000
 391  H271  C27  C25   109.99  3.000
 391  C21   N26  C25   115.71  3.000
 391  O17   C21  N26   115.25  3.000
 391  O17   C21  N22   117.11  3.000
 391  N26   C21  N22   127.64  3.000
 391  C14   O17  C21   116.55  3.000
 391  C13   C14  C15   120.96  3.000
 391  C13   C14  O17   119.83  3.000
 391  C15   C14  O17   119.21  3.000
 391  H15   C15  C16   120.14  3.000
 391  H15   C15  C14   120.40  3.000
 391  C16   C15  C14   119.46  3.000
 391  H16   C16  C11   120.61  3.000
 391  H16   C16  C15   119.49  3.000
 391  C11   C16  C15   119.90  3.000
 391  H13   C13  C12   119.85  3.000
 391  H13   C13  C14   120.55  3.000
 391  C12   C13  C14   119.57  3.000
 391  H12   C12  C11   120.59  3.000
 391  H12   C12  C13   119.50  3.000
 391  C11   C12  C13   119.88  3.000
 391  N3    C11  C12   119.81  3.000
 391  N3    C11  C16   120.01  3.000
 391  C12   C11  C16   120.19  3.000
 391  C2    N3   C4    106.80  3.000
 391  C2    N3   C11   126.56  3.000
 391  C4    N3   C11   126.64  3.000
 391  H4    C4   C5    132.04  3.000
 391  H4    C4   N3    122.43  3.000
 391  C5    C4   N3    105.51  3.000
 391  H5    C5   NFE   121.99  3.000
 391  H5    C5   C4    127.68  3.000
 391  NFE   C5   C4    110.33  3.000
 391  C2    NFE  C5    105.57  3.000
 391  H2    C2   NFE   126.01  3.000
 391  H2    C2   N3    122.17  3.000
 391  NFE   C2   N3    111.80  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 391  CONST_01  C33   C32  C31  C36     0.00   0.0  0
 391  CONST_02  C33   C34  C35  C36     0.00   0.0  0
 391  CONST_03  C32   C31  C36  C35     0.00   0.0  0
 391  CONST_04  C32   C33  C34  C35     0.00   0.0  0
 391  CONST_05  C31   C36  C35  C34     0.00   0.0  0
 391  CONST_06  C31   C32  C33  C34     0.00   0.0  0
 391  CONST_07  N26   C25  C24  C23     0.00   0.0  0
 391  CONST_08  N26   C21  N22  C23     0.00   0.0  0
 391  CONST_09  C25   C24  C23  N22     0.00   0.0  0
 391  CONST_10  C25   N26  C21  N22     0.00   0.0  0
 391  CONST_11  C21   N22  C23  C24     0.00   0.0  0
 391  CONST_12  C21   N26  C25  C24     0.00   0.0  0
 391  CONST_13  C11   C16  C15  C14     0.00   0.0  0
 391  CONST_14  C11   C12  C13  C14     0.00   0.0  0
 391  CONST_15  C12   C13  C14  C15     0.00   0.0  0
 391  CONST_16  C12   C11  C16  C15     0.00   0.0  0
 391  CONST_17  N3    C11  C16  C15   180.00   0.0  0
 391  CONST_18  C13   C14  C15  C16     0.00   0.0  0
 391  CONST_19  C13   C12  C11  C16     0.00   0.0  0
 391  CONST_22  N3    C11  C12  C13   180.00   0.0  0
 391  CONST_25  C5    C4   N3   C11   180.00   0.0  0
 391  CONST_26  NFE   C2   N3   C11   180.00   0.0  0
 391  CONST_27  NFE   C5   C4   N3      0.00   0.0  0
 391  CONST_28  C5    NFE  C2   N3      0.00   0.0  0
 391  CONST_29  NFE   C2   N3   C4      0.00   0.0  0
 391  CONST_30  C2    NFE  C5   C4      0.00   0.0  0
 391  CONST_31  C2    N3   C4   C5      0.00   0.0  0
 391  CONST_32  O28   C31  C36  C35   180.00   0.0  0
 391  CONST_33  O28   C31  C32  C33   180.00   0.0  0
 391  CONST_34  C25   C24  C23  O28   180.00   0.0  0
 391  CONST_35  C21   N22  C23  O28   180.00   0.0  0
 391  CONST_36  C27   C25  C24  C23   180.00   0.0  0
 391  CONST_37  O17   C21  N22  C23   180.00   0.0  0
 391  CONST_38  O17   C21  N26  C25   180.00   0.0  0
 391  CONST_39  C21   N26  C25  C27   180.00   0.0  0
 391  CONST_40  C16   C15  C14  O17   180.00   0.0  0
 391  CONST_41  C12   C13  C14  O17   180.00   0.0  0
 391  CONST_42  H32   C32  C31  C36   180.00   0.0  0
 391  CONST_43  H33   C33  C34  C35   180.00   0.0  0
 391  CONST_44  H36   C36  C35  O39     0.00   0.0  0
 391  CONST_45  H24   C24  C23  N22   180.00   0.0  0
 391  CONST_46  H16   C16  C15  C14   180.00   0.0  0
 391  CONST_47  H12   C12  C13  C14   180.00   0.0  0
 391  CONST_48  H13   C13  C14  C15   180.00   0.0  0
 391  CONST_49  H15   C15  C14  C13   180.00   0.0  0
 391  CONST_50  H4    C4   N3   C11     0.00   0.0  0
 391  CONST_51  H2    C2   N3   C11     0.00   0.0  0
 391  CONST_52  H5    C5   C4   N3    180.00   0.0  0
 391  Var_01    O37   C38  O39  C35   -15.57  30.0  1
 391  Var_02    C34   C35  O39  C38     9.83  30.0  1
 391  Var_03    C33   C34  O37  C38   171.21  30.0  1
 391  Var_04    C24   C23  O28  C31  -179.80  30.0  2
 391  Var_05    C15   C14  O17  C21  -104.69  30.0  2
 391  Var_06    H271  C27  C25  C24   115.20  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 391  plan-1  C11  0.020
 391  plan-1  N3   0.020
 391  plan-1  C4   0.020
 391  plan-1  C5   0.020
 391  plan-1  NFE  0.020
 391  plan-1  C2   0.020
 391  plan-1  H4   0.020
 391  plan-1  H5   0.020
 391  plan-1  H2   0.020
 391  plan-2  O28  0.020
 391  plan-2  C23  0.020
 391  plan-2  N22  0.020
 391  plan-2  C24  0.020
 391  plan-2  C25  0.020
 391  plan-2  C27  0.020
 391  plan-2  N26  0.020
 391  plan-2  C21  0.020
 391  plan-2  O17  0.020
 391  plan-2  H24  0.020
 391  plan-3  C36  0.020
 391  plan-3  C35  0.020
 391  plan-3  O39  0.020
 391  plan-3  O37  0.020
 391  plan-3  C34  0.020
 391  plan-3  C33  0.020
 391  plan-3  C32  0.020
 391  plan-3  C31  0.020
 391  plan-3  O28  0.020
 391  plan-3  H36  0.020
 391  plan-3  H33  0.020
 391  plan-3  H32  0.020
 391  plan-4  O17  0.020
 391  plan-4  C14  0.020
 391  plan-4  C15  0.020
 391  plan-4  C16  0.020
 391  plan-4  C13  0.020
 391  plan-4  C12  0.020
 391  plan-4  C11  0.020
 391  plan-4  N3   0.020
 391  plan-4  H15  0.020
 391  plan-4  H16  0.020
 391  plan-4  H13  0.020
 391  plan-4  H12  0.020

